It also seems to me worth adding: the Children of Israel did this after a revelation from the Creator of all and the God of morality (after the Revelation at Mount Sinai), and indeed today, when we are not certain of its truth, we have no moral right to do so (and a person must examine himself carefully and without bias). But how do they know that they were commanded to do this?
Rabbi Moshe Shapira would always point out that the way to check the source of a decision is by examining character traits. In other words, the fact that in Gaza they rejoice and exult over the blood of a murdered Jewish baby proves that truth and justice are not what guide them.

It is not similar at all.
Maimonides wrote: “One does not wage war against any person in the world until first offering peace, whether an optional war or a commanded war, as it says, ‘When you approach a city to fight against it, you shall call out to it for peace.’ If they make peace and accept the seven commandments that the descendants of Noah were commanded regarding, no one among them is killed, and they become tributaries, as it says, ‘They shall be subject to tribute to you and serve you.’

Joshua sent three letters before entering the Land: first he sent them, ‘Whoever wishes to flee, let him flee’; then he sent again, ‘Whoever wishes to make peace, let him make peace’; and then he sent again, ‘Whoever wishes to make war, let him do so.’”

Avner, meaning that what’s missing for you is that Hamas should publish an option for Israelis to pay tribute and be slaves of the Palestinians, and also give Jews the option of fleeing the land—and only after the Jews in Israel surprisingly refuse would Hamas have moral permission to massacre them?

Another note—the Torah testifies that the whole world heard about God’s revelation to the Children of Israel, so apparently they should have accepted that, no?

Of course, the question is: if you were to direct your question to Hamas themselves—do they think they are moral, what would they answer? To the best of my knowledge, their answer is religious, and then we are back to the worn-out issue of religion versus morality, and then Rabbi Michi will come and say that morality has a status like religion (and maybe even more than religion), and that is the reason Hamas terrorists are immoral. But the problem is that the Hamas terrorists themselves do not think that way (that is, in their view religion comes before morality). If so, in the end the reason they are not moral is simply that they are mistaken, and so the only question left is whether in your opinion the Children of Israel were mistaken or not.
(And now the Rema will come and say: have I not already pointed out to you many times that one must not confuse facts with values—and we will say that we have not merited to understand whether this very claim is itself a factual claim or a value claim, and this is not the place to elaborate.)

Hello, and thank you for this fruitful discussion,

Below is a quote from a reply that Rabbi Moshe Rat also wrote to me on this matter:
“The answer is very simple. Our ancestors were in no way similar to Hamas, who slaughtered innocent people, but rather to IDF soldiers who went out to war against a culture of evil. The peoples of Canaan were not just innocent simple folk, but a corrupt culture in which masses of babies and children were sacrificed to demons and idols, girls were given over to cultic prostitution in temples, and they were steeped in every kind of moral abomination. God tells Abraham that only in the fourth generation will his descendants return to the land, ‘for the iniquity of the Amorite is not yet complete’—meaning that only when the measure of their sins was full was destruction decreed upon them. And even when the Children of Israel arrived in the land, Joshua sent letters in which he gave everyone the option of making peace and living in peace, on condition that they submit to Israel and accept upon themselves the seven Noahide commandments. Had they done so, they could have remained alive. So it is obvious why the comparison to Hamas does not even get off the ground, and that is even before speaking about Hamas’s torture and cruel abuse, which did not exist among the Children of Israel.”

And regarding the killing of the children he wrote:
“First, one must understand that war is a confrontation between peoples, between collectives, and not between individuals. Consequently, the relation to anyone belonging to the enemy people is not as to a private person but as part of the enemy—just as when you fight someone, you also strike parts of his body that are not directly attacking you.
Second, there is corruption that passes through genes or souls, and it will necessarily also be manifested in the descendants of those peoples, such as the peoples of Canaan and Amalek. Therefore the commandment came to destroy them as well.
Third, technically there is no possibility for babies and children to survive on their own, and to impose on the people of Israel the burden of raising all the descendants of the Canaanites is not reasonable. Besides, presumably when they grow up and hear what was done to their forefathers, they will want revenge. Therefore, killing them is called for.”

Maybe that is a reasonable answer regarding the Canaanites, but regarding Amalek there is no answer here—unless Rabbi Rat claims that Amalek too was among the Canaanite peoples.
But the bigger problem is the many places in the Hebrew Bible where there is immoral warfare. For example, in every war there is an obligation to kill all the males (not specifically a war against the Canaanites, where every person must be killed), as written at the end of Parashat Shoftim. And in general, in tractate Berakhot it is written that the justification for war can be purely economic.

Maybe the words of Maimonides that Avner quoted above are the answer. It seems that according to Maimonides, in any war the justification for killing is if the nation does not accept upon itself the seven Noahide commandments.